Locus 4346

Sequence ID dm3.chr2R
Location 12,375,327 – 12,375,424
Length 97
Max. P 0.971548
window5957 window5958

overview

Window 7

Location 12,375,327 – 12,375,424
Length 97
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 61.58
Shannon entropy 0.65740
G+C content 0.36982
Mean single sequence MFE -21.04
Consensus MFE -9.68
Energy contribution -9.84
Covariance contribution 0.16
Combinations/Pair 1.39
Mean z-score -1.13
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.838169
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12375327 97 + 21146708
-------------GAAUGCUAGAAUGUCA-AUUUAGACUAUCUUCUUUGGAAAGAAGACUUUUAUAGAGUUUCAUGCGUAAAGCUUUAUACCCUCUACAAGGGUAUACAAA
-------------(((..(((....(((.-.....)))..(((((((....)))))))......)))...)))..((.....))..((((((((.....)))))))).... ( -21.50, z-score =  -1.65, R)
>droSim1.chr2R 11113978 97 + 19596830
-------------GAAUGCUAGAAUGUCA-AUAUACACUAUCUUCAGUAGAAAGAAGGCUUUCUCAGAGUUUCAAGCAGAUAGCUUUAUACCCUCUGCAAGGGUAUAAUAA
-------------...((((.(((..((.-......(((......)))((((((....))))))..))..))).)))).......(((((((((.....)))))))))... ( -22.10, z-score =  -1.20, R)
>droSec1.super_1 9879248 76 + 14215200
-----------------------------------AGUAGAAGUCAGUAAAAAGAAGGCUUUUUCAGAGUUUCAUGCAUAAAGCUUAAUACCCUCUGCAAGGGUAUAAAAA
-----------------------------------.(.(((((((...........))))))).).((((((........)))))).(((((((.....)))))))..... ( -15.50, z-score =  -1.37, R)
>droYak2.chr2R 4532502 111 - 21139217
AGAGGUGCGAAUCGAACGUUUCCGACUUACACAUACACUACCUUCAGUAGGAAUAACGCAUUCAUGAAGUUUCUUGCAGAUAGCCUUAUACCCUUUGCAAGGGUAUACAAU
.(((((((((.(((........)))................(((((....((((.....)))).)))))....)))).....)))))(((((((.....)))))))..... ( -22.20, z-score =  -0.62, R)
>droEre2.scaffold_4845 9107413 107 - 22589142
AACUGUGCGAAUCGGACGUUUCCGACUUA----UACACUACCUUCAGUAGGAGAAAGGCUUUUAUUAAGUUUCAUGCUGAUAACCUUAAGCCCUUUGCAAGGGUAUACAAU
...((((..(.(((((....))))).)..----))))......((((((.(((....((((.....))))))).)))))).........(((((.....)))))....... ( -23.90, z-score =  -0.82, R)
>consensus
_____________GAACGCUACAAACUCA_A__UACACUACCUUCAGUAGAAAGAAGGCUUUUAUAGAGUUUCAUGCAGAUAGCUUUAUACCCUCUGCAAGGGUAUACAAA
.....................................((((.....)))).....((((((.....))))))..............((((((((.....)))))))).... ( -9.68 =  -9.84 +   0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,375,327 – 12,375,424
Length 97
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 61.58
Shannon entropy 0.65740
G+C content 0.36982
Mean single sequence MFE -22.30
Consensus MFE -10.94
Energy contribution -11.90
Covariance contribution 0.96
Combinations/Pair 1.29
Mean z-score -1.49
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971548
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12375327 97 - 21146708
UUUGUAUACCCUUGUAGAGGGUAUAAAGCUUUACGCAUGAAACUCUAUAAAAGUCUUCUUUCCAAAGAAGAUAGUCUAAAU-UGACAUUCUAGCAUUC-------------
....(((((((((...))))))))).........((..(((...........((((((((....)))))))).(((.....-.))).)))..))....------------- ( -24.00, z-score =  -3.04, R)
>droSim1.chr2R 11113978 97 - 19596830
UUAUUAUACCCUUGCAGAGGGUAUAAAGCUAUCUGCUUGAAACUCUGAGAAAGCCUUCUUUCUACUGAAGAUAGUGUAUAU-UGACAUUCUAGCAUUC-------------
...((((((((((...)))))))))).(((((((.........((..((((((....))))))...)))))))))......-................------------- ( -21.90, z-score =  -1.14, R)
>droSec1.super_1 9879248 76 - 14215200
UUUUUAUACCCUUGCAGAGGGUAUUAAGCUUUAUGCAUGAAACUCUGAAAAAGCCUUCUUUUUACUGACUUCUACU-----------------------------------
.....((((((((...))))))))...((.....))..(((..((..((((((....))))))...)).)))....----------------------------------- ( -12.50, z-score =  -0.89, R)
>droYak2.chr2R 4532502 111 + 21139217
AUUGUAUACCCUUGCAAAGGGUAUAAGGCUAUCUGCAAGAAACUUCAUGAAUGCGUUAUUCCUACUGAAGGUAGUGUAUGUGUAAGUCGGAAACGUUCGAUUCGCACCUCU
...((((((.((((((...(((.....)))...))))))...(((((.(((((...)))))....)))))...))))))(((..(((((((....)))))))..))).... ( -28.80, z-score =  -1.52, R)
>droEre2.scaffold_4845 9107413 107 + 22589142
AUUGUAUACCCUUGCAAAGGGCUUAAGGUUAUCAGCAUGAAACUUAAUAAAAGCCUUUCUCCUACUGAAGGUAGUGUA----UAAGUCGGAAACGUCCGAUUCGCACAGUU
.((((((((((((.((((((((((.(((((.((.....))))))).....)))))))).......))))))..)))))----)))((((((....)))))).......... ( -24.31, z-score =  -0.85, R)
>consensus
UUUGUAUACCCUUGCAGAGGGUAUAAAGCUAUCUGCAUGAAACUCUAUAAAAGCCUUCUUUCUACUGAAGAUAGUGUA__U_UAACACGCAAACAUUC_____________
....(((((((((...)))))))))..((.....))................((((((........))))))....................................... (-10.94 = -11.90 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:27:25 2011